Updating rule pca

CCBR · Oct 13, 2018 · 11e049b · 11e049b
1 parent b97bf16
commit 11e049b
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/Results-template/Scripts/pcacall.R b/Results-template/Scripts/pcacall.R
@@ -1,4 +1,4 @@
-# Example Usgae: Rscript pcacall.R 'DEG_cntrl-test_0.5_2' 'STAR_files/sampletable.txt' 'DEG_cntrl-test_0.5_2/RawCountFile_RSEM_genes_filtered.txt' 'hg19seDEG' 'Enter CCBR Project Description and Notes here.'
+# Example Usgae: Rscript pcacall.R 'DEG_cntrl-test_0.5_2' 'outfilename.html'  'STAR_files/sampletable.txt' 'DEG_cntrl-test_0.5_2/RawCountFile_RSEM_genes_filtered.txt' 'hg19seDEG' 'Enter CCBR Project Description and Notes here.'
 ## grab args
 args <- commandArgs(trailingOnly = TRUE)
 DIR <- args[1]

diff --git a/Rules/rnaseq.snakefile b/Rules/rnaseq.snakefile
@@ -261,7 +261,7 @@ rule pca:
     file1=join(workpath,star_dir,"sampletable.txt"),
     file2=join(workpath,"DEG_{dtype}","RawCountFile_RSEM_genes_filtered.txt"),
   output: 
-    join(workpath,"DEG_{dtype}","PcaReport.html")
+    outhtml=join(workpath,"DEG_{dtype}","PcaReport.html")
   params: 
     rname='pl:pca',
     batch='--mem=24g --time=10:00:00',
@@ -278,7 +278,7 @@ cp {params.rscript1} {params.outdir}
 cp {params.rscript2} {params.outdir}
 cd {params.outdir}
 module load {params.rver}
-Rscript pcacall.R '{params.outdir}' '{input.file1}' '{input.file2}' '{params.projectId}' '{params.projDesc}'
+Rscript pcacall.R '{params.outdir}' '{output.outhtml}' '{input.file1}' '{input.file2}' '{params.projectId}' '{params.projDesc}'
 """
 
 rule vennDiagram: